Followup to this - if you do #1 the right way you essentially result in the same system as #3 with FreePBX 17
For FreePBX 16, #1 is equivalent to using the canned distro (since in FreePBX 16 there is no installation script) and removing Asterisk from it using apt remove. There is no equivalent to #3 for FreePBX 16.
Note that one of the cons for the #3 method is that a manual build of Asterisk with a custom module may introduce an interdependency in modules that may run into a default setting of FreePBX to not load that dependent module. (there’s about 5 modules that are restricted from loading by default in FreePBX) So go through the FreePBX config -thoroughly- once it’s running.